ClinVar Miner

Submissions for variant NM_001161403.3(LIMS2):c.882C>A (p.Asn294Lys)

gnomAD frequency: 0.00038  dbSNP: rs149101001
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000652650 SCV000774521 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2W 2024-10-28 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 316 of the LIMS2 protein (p.Asn316Lys). This variant is present in population databases (rs149101001, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with LIMS2-related conditions. ClinVar contains an entry for this variant (Variation ID: 542250). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt LIMS2 protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Revvity Omics, Revvity RCV000652650 SCV003814630 likely benign Autosomal recessive limb-girdle muscular dystrophy type 2W 2023-08-29 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV004692045 SCV005187903 uncertain significance not provided criteria provided, single submitter not provided

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